IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners

Abstract

IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number of entries in IDEAL has almost tripled (120 to 340). In addition to the increase in quantity, the quality of IDEAL has been significantly improved. The new IDEAL incorporates the interactions of IDPs and their binding partners more explicitly, and illustrates the protein–protein interaction (PPI) networks and the structures of protein complexes. Redundant experimental data are arranged based on the clustering of Protein Data Bank entries, and similar sequences with the same binding mode are grouped. As a result, the new IDEAL presents more concise and informative experimental data. Nuclear magnetic resonance (NMR) disorder is annotated in a systematic manner, by identifying the regions with large deviations among the NMR models. The ordered/disordered and new domain predictions by DICHOT are available, as well as the domain assignments by HMMER. Some examples of the PPI networks and the highly deviated regions derived from NMR models will be described, together with other advances. These enhancements will facilitate deeper understanding of IDPs, in terms of their flexibility, plasticity and promiscuity.

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

“…109 The current release of this database (as of June 2016) contains 713 proteins with 464,962 total residues and 23,207 disordered residues. The IDEAL interface offers a blast engine that enables efficient retrieval of existing annotations pertaining to potential disordered regions within a query sequence.…”

Predicting Conformational Disorder

“…Compare the annotations of the selected entry with the boundaries obtained in step 4 . IDEAL ( http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ blast.html ) is the second database, in terms of size, dedicated to proteins whose disorder has been experimentally assessed [ 22 ]. The total number of proteins in IDEAL is 582 (as of June 2015).…”

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

“…IDEAL (17) indicates those ID regions that undergo coupled folding and binding, based on Protein Data Bank (PDB) evidence. Those IDRs however, that remain disordered in the bound form are lacking.…”